For what it's worth I used to have an s2000 for a number of years (have a 370z GT coupe now) and I had a cover for that.
Trouble is with an outdoor cover no matter how good a fit, you get small movement from the nylon or tyvek fabric against your paintwork in the 4 corner areas of your car. Eventually it'll start rubbing away at your paintwork in those areas.
I stopped using it after a series of windy days/nights.
If you protect your roof by cleaning it and sealing it with waterproof chemicals (the autoglym stuff works fine) then your roof will come to no harm.
I had my s2 for 4 years and the roof was in good condition when I sold it